FASTQC and MultiQC - Revision history

Rf at 13:30, 18 July 2017

2017-07-18T13:30:00Z

Rf at 12:44, 18 July 2017

2017-07-18T12:44:38Z

Rf at 14:00, 13 April 2017

2017-04-13T14:00:55Z

Rf at 13:51, 13 April 2017

2017-04-13T13:51:06Z

Rf at 13:50, 13 April 2017

2017-04-13T13:50:34Z

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Rf: Replaced content with " No Name [/home/nutria], b1, wiki |Introduction |FastQC = . |fastqc's help file |MultiQC |multiqc's help file"

2017-04-13T13:50:01Z

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Rf at 13:43, 13 April 2017

2017-04-13T13:43:15Z

Rf at 16:11, 14 December 2016

2016-12-14T16:11:07Z

Rf at 15:43, 6 July 2016

2016-07-06T15:43:48Z

Rf at 15:43, 6 July 2016

2016-07-06T15:43:16Z

@@ Line 1: / Line 1: @@
 =Introduction=
-Assessment of short read quality. FastQC carries out analysis on a single readset, usually represented by a single fastq or fastq.gz file. MultiQC uses the output of FASTQC to aggregate the FastQC quality indicators of the different reads together, to allo inter-readset comparisons.
+Assessment of short read quality. FastQC carries out analysis on a single readsets, usually represented by a single fastq or fastq.gz file. It is of no concern whether the reads come from single or paired libraries. FastQC calls these sequences, rather than reads.
 = FastQC =

@@ Line 11: / Line 11: @@
 It gives quite detailed graphs on the nature of the readset, and details to the different graphics can be found at the following link: http://www.bioinformatics.babraham.ac.uk/projects/fastqc/Help/3%20Analysis%20Modules/
-== fastqc's help file ==
+= FastQC's modules =
   SYNOPSIS

@@ Line 1: / Line 1: @@
 =Introduction=
-Assessment of short read quality
+Assessment of short read quality. FastQC carries out analysis on a single readset, usually represented by a single fastq or fastq.gz file. MultiQC uses the output of FASTQC to aggregate the FastQC quality indicators of the different reads together, to allo inter-readset comparisons.
 = FastQC =

@@ Line 121: / Line 121: @@
 * M Seqs, millions of sequences
-= multiqc's help file =
+== multiqc's help file ==
   Usage: multiqc [OPTIONS] <analysis directory>

@@ Line 1: / Line 1: @@
 =Introduction=
-Quality visualization
+Assessment of short read quality
 =MultiQC =
@@ Line 23: / Line 21: @@
 * Length
 * M Seqs, millions of sequences
 = multiqc's help file =

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 =MultiQC =
-Under general statistics we get the following headings:
+A relatively new tool that aggregates the output of FASTQC into one report.
 * Sample Name

← Older revision		Revision as of 15:43, 6 July 2016
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	= multiqc's help file =		= multiqc's help file =

−		+	Usage: multiqc [OPTIONS] <analysis directory>
		+
		+	MultiQC aggregates results from bioinformatics analyses across many
		+	samples into a single report.
		+
		+	It searches a given directory for analysis logs and compiles a HTML
		+	report. It's a general use tool, perfect for summarising the output from
		+	numerous bioinformatics tools.
		+
		+	To run, supply with one or more directory to scan for analysis results.
		+	To run here, use 'multiqc .'
		+
		+	See http://multiqc.info for more details.
		+
		+	Author: Phil Ewels (http://phil.ewels.co.uk)
		+
		+	Options:
		+	-f, --force Overwrite any existing reports
		+	-d, --dirs Prepend directory to sample names
		+	-s, --fullnames Do not clean the sample names (leave as full
		+	file name)
		+	-i, --title TEXT Report title. Printed as page header, used
		+	for filename if not otherwise specified.
		+	-n, --filename TEXT Report filename. Use 'stdout' to print to
		+	standard out.
		+	-o, --outdir TEXT Create report in the specified output
		+	directory.
		+	-t, --template [default\|default_dev\|geo\|simple]
		+	Report template to use.
		+	-x, --ignore TEXT Ignore analysis files (glob expression)
		+	-e, --exclude [module name] Do not use this module. Can specify multiple
		+	times.
		+	-m, --module [module name] Use only this module. Can specify multiple
		+	times.
		+	--data-dir / --no-data-dir Specify whether the parsed data directory
		+	should be created.
		+	-k, --data-format [tsv\|yaml\|json]
		+	Output parsed data in a different format
		+	-z, --zip-data-dir Compress the data directory.
		+	--flat Use only flat plots (static images)
		+	--interactive Use only interactive plots (HighCharts
		+	Javascript)
		+	-c, --config PATH Specific config file to load, after those in
		+	MultiQC dir / home dir / working dir.
		+	-v, --verbose Increase output verbosity.
		+	-q, --quiet Only show log warnings
		+	--version Show the version and exit.
		+	-h, --help Show this message and exit.